[Bioperl-l] Module to draw transmembrane protein topology
t.nugent at cs.ucl.ac.uk
Tue Feb 20 10:50:10 EST 2007
Labeling of inside/outside and membrane is already possible via
-inside_label, -outside_label and -membrane_label tags, defaults are
intracellular, extracellular and plasma membrane.
Was definitely going to add an input/parser for MEMSAT, developed here
at UCL, and probably a few other popular TM predictors too, e.g.
PHOBIUS, TMHMM etc. Can already accept topology in the string format
used by OPM (http://opm.phar.umich.edu/).
Chris Fields wrote:
> Sorry, I sent that last one off prematurely.
> I could see this being used as a very useful utility if a Bioperl object
> had SeqFeatures which described transmembrane regions, or if output from
> something like TMHMM were parsed and used for input. Don't know if it's
> included, but if not you probably should allow labeling of the
> intracellular/extracellular space to designate periplasmic space,
> mitochondrial matrix, thylakoid, etc.
> I think Bio::Graphics namespace is definitely the place to go. If I
> ever get around to writing up the RNA structural stuff I may put
> something there myself.
> On Feb 20, 2007, at 8:31 AM, Tim Nugent wrote:
>> Thanks Chris, glad it's appreciated.
>> Is there anything else I can do? If anyone has any requests/suggestions
>> please let me know too.
>> Best wishes,
Tim Nugent (MRes)
Department of Computer Science
University College London
London WC1E 6BT
t.nugent at ucl.ac.uk
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